Early and long-term responses of intestinal microbiota and metabolites to 131I treatment in differentiated thyroid cancer patients.

BACKGROUND: Multiple high doses of 131I therapy in patients with differentiated thyroid cancer (DTC) might disrupt the balance of gut microbiota and metabolites. This study aimed to investigate the alterations of intestinal bacteria and metabolism over two courses of 131I therapy, explore the interactions, and construct diagnostic models reflecting enteric microecology based on 131I therapy. METHODS: A total of 81 patients were recruited for the first 131I therapy (131I-1st), among whom 16 received a second course (131I-2nd) after half a year. Fecal samples were collected 1 day before (Pre-131I-1st/2nd) and 3 days after (Post-131I-1st/2nd) 131I therapy for microbiome (16S rRNA gene sequencing) and metabolomic (LC-MS/MS) analyses. RESULTS: A total of six microbial genera and 11 fecal metabolites enriched in three pathways were identified to show significant differences between Pre-131I-1st and other groups throughout the two courses of 131I treatment. In the Post-131I-1st group, the beneficial bacteria Bifidobacterium, Lachnoclostridium, uncultured_bacterium_f_Lachnospiraceae, and Lachnospiraceae_UCG004 were abundant and the radiation-sensitive pathways of linoleic acid (LA), arachidonic acid, and tryptophan metabolism were inhibited compared with the Pre-131I-1st group. Compared with the Pre-131I-1st group, the Pre-131I-2nd group exhibited a reduced diversity of flora and differentially expressed metabolites, with a low abundance of beneficial bacteria and dysregulated radiation-sensitive pathways. However, less significant differences in microbiota and metabolites were found between the Pre/Post-131I-2nd groups compared with those between the Pre/Post-131I-1st groups. A complex co-occurrence was observed between 6 genera and 11 metabolites, with Lachnoclostridium, Lachnospiraceae_UCG004, Escherichia-Shigella, and LA-related metabolites contributing the most. Furthermore, combined diagnostic models of charactered bacteria and metabolites answered well in the early, long-term, and dose-dependent responses for 131I therapy. CONCLUSIONS: Different stages of 131I therapy exert various effects on gut microecology, which play an essential role in regulating radiotoxicity and predicting the therapeutic response.

The CsPPR gene with RNA-editing function involved in leaf color asymmetry of the reciprocal hybrids derived from Cucumis sativus and C. hystrix.

MAIN CONCLUSION: The leaf color asymmetry found in the reciprocal hybrids C. hystrix × C. sativus (HC) and C. sativus × C. hystrix (CH) could be influenced by the CsPPR gene (CsaV3_1G038250.1). Most angiosperm organelles are maternally inherited; thus, the reciprocal hybrids usually exhibit asymmetric phenotypes that are associated with the maternal parent. However, there are two sets of organelle genomes in the plant cytoplasm, and the mechanism of reciprocal differences are more complex and largely unknown, because the chloroplast genes are involved besides mitochondrial genes. Cucumis spp. contains the species, i.e., cucumber and melon, which chloroplasts and mitochondria are maternally inherited and paternally inherited, respectively, serving as good materials for the study of reciprocal differences. In this study, leaf color asymmetry was observed in the reciprocal hybrids (HC and CH) derived from C. sativus (2n = 14, CC) and C. hystrix (2n = 24, HH), where the leaves of HC were found to have reduced chlorophyll content, abnormal chloroplast structure and lower photosynthetic capacity. Transcriptomic analysis revealed that the chloroplast development-related genes were differentially expressed in leaf color asymmetry. Genetic analysis showed that leaf color asymmetry was caused by the maternal chloroplast genome. Comparative analysis of chloroplast genomes revealed that there was no mutation in the chloroplast genome during interspecific hybridization. Moreover, a PPR gene (CsaV3_1G038250.1) with RNA-editing function was found to be involved in the regulation of leaf color asymmetry. These findings provide new insights into the regulatory mechanisms of asymmetric phenotypes in plant reciprocal crosses.

Disrupted gut microecology after high-dose 131I therapy and radioprotective effects of arachidonic acid supplementation.

BACKGROUND: Despite the potential radiotoxicity in differentiated thyroid cancer (DTC) patients with high-dose 131I therapy, the alterations and regulatory mechanisms dependent on intestinal microecology remain poorly understood. We aimed to identify the characteristics of the gut microbiota and metabolites in DTC patients suffering from high-dose 131I therapy and explore the radioprotective mechanisms underlying arachidonic acid (ARA) treatment. METHODS: A total of 102 patients with DTC were recruited, with fecal samples collected before and after 131I therapy for microbiome and untargeted and targeted metabolomic analyses. Mice were exposed to total body irradiation with ARA replenishment and antibiotic pretreatment and were subjected to metagenomic, metabolomic, and proteomic analyses. RESULTS: 131I therapy significantly changed the structure of gut microbiota and metabolite composition in patients with DTC. Lachnospiraceae were the most dominant bacteria after 131I treatment, and metabolites with decreased levels and pathways related to ARA and linoleic acid were observed. In an irradiation mouse model, ARA supplementation not only improved quality of life and recovered hematopoietic and gastrointestinal systems but also ameliorated oxidative stress and inflammation and preserved enteric microecology composition. Additionally, antibiotic intervention eliminated the radioprotective effects of ARA. Proteomic analysis and ursolic acid pretreatment showed that ARA therapy greatly influenced intestinal lipid metabolism in mice subjected to irradiation by upregulating the expression of hydroxy-3-methylglutaryl-coenzyme A synthase 1. CONCLUSION: These findings highlight that ARA, as a key metabolite, substantially contributes to radioprotection. Our study provides novel insights into the pivotal role that the microbiota-metabolite axis plays in radionuclide protection and offers effective biological targets for treating radiation-induced adverse effects.

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber.

Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.

Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis.

Karyotype dynamics driven by complex chromosome rearrangements constitute a fundamental issue in evolutionary genetics. The evolutionary events underlying karyotype diversity within plant genera, however, have rarely been reconstructed from a computed ancestral progenitor. Here, we developed a method to rapidly and accurately represent extant karyotypes with the genus, Cucumis, using highly customizable comparative oligo-painting (COP) allowing visualization of fine-scale genome structures of eight Cucumis species from both African-origin and Asian-origin clades. Based on COP data, an evolutionary framework containing a genus-level ancestral karyotype was reconstructed, allowing elucidation of the evolutionary events that account for the origin of these diverse genomes within Cucumis. Our results characterize the cryptic rearrangement hotspots on ancestral chromosomes, and demonstrate that the ancestral Cucumis karyotype (n = 12) evolved to extant Cucumis genomes by hybridizations and frequent lineage- and species-specific genome reshuffling. Relative to the African species, the Asian species, including melon (Cucumis melo, n = 12), Cucumis hystrix (n = 12) and cucumber (Cucumis sativus, n = 7), had highly shuffled genomes caused by large-scale inversions, centromere repositioning and chromothripsis-like rearrangement. The deduced reconstructed ancestral karyotype for the genus allowed us to propose evolutionary trajectories and specific events underlying the origin of these Cucumis species. Our findings highlight that the partitioned evolutionary plasticity of Cucumis karyotype is primarily located in the centromere-proximal regions marked by rearrangement hotspots, which can potentially serve as a reservoir for chromosome evolution due to their fragility.

Salinity, waterlogging, and elevated [CO2] interact to induce complex responses in cultivated and wild tomato.

The effects of individual climatic factors on crops are well documented, whereas the interaction of such factors in combination has received less attention. The frequency of salinity and waterlogging stress is increasing with climate change, accompanied by elevated CO2 concentration (e[CO2]). This study explored how these three variables interacted and affected two tomato genotypes. Cultivated and wild tomato (Solanum lycopersicum and Solanum pimpinellifolium) were grown at ambient [CO2] and e[CO2], and subjected to salinity, waterlogging, and combined stress. Leaf photosynthesis, chlorophyll fluorescence, quenching analysis, pigment, and plant growth were analyzed. The response of tomatoes depended on both genotype and stress type. In cultivated tomato, photosynthesis was inhibited by salinity and combined stress, whereas in wild tomato, both salinity and waterlogging stress, alone and in combination, decreased photosynthesis. e[CO2] increased photosynthesis and biomass of cultivated tomato under salinity and combined stress compared with ambient [CO2]. Differences between tomato genotypes in response to individual and combined stress were observed in key photosynthetic and growth parameters. Hierarchical clustering and principal component analysis revealed genetic variations of tomatoes responding to the three climatic factors. Understanding the interacting effects of salinity and waterlogging with e[CO2] in tomato will facilitate improvement of crop resilience to climate change.

Dominant and Priming Role of Waterlogging in Tomato at e[CO2] by Multivariate Analysis.

The frequency of waterlogging episodes has increased due to unpredictable and intense rainfalls. However, less is known about waterlogging memory and its interaction with other climate change events, such as elevated CO2 concentration (e[CO2]). This study investigated the combined effects of e[CO2] and two rounds of waterlogging stress on the growth of cultivated tomato (Solanum lycopersicum) and wild tomato (S. pimpinellifolium). The aim is to elucidate the interaction between genotypes and environmental factors and thereby to improve crop resilience to climate change. We found that two rounds of treatments appeared to induce different acclimation strategies of the two tomato genotypes. S. pimpinellifolium responded more negatively to the first-time waterlogging than S. lycopersicum, as indicated by decreased photosynthesis and biomass loss. Nevertheless, the two genotypes respond similarly when waterlogging stress recurred, showing that they could maintain a higher leaf photosynthesis compared to single stress, especially for the wild genotype. This showed that waterlogging priming played a positive role in stress memory in both tomato genotypes. Multivariate analysis showed that waterlogging played a dominant role when combined with [CO2] for both the cultivated and wild tomato genotypes. This work will benefit agricultural production strategies by pinpointing the positive effects of e[CO2] and waterlogging memory.

Transcriptomic and Physiological Analyses Reveal Potential Genes Involved in Photoperiod-Regulated ß-Carotene Accumulation Mechanisms in the Endocarp of Cucumber (Cucumis sativus L.) Fruit.

The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit ß-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with ß-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced ß-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, ß-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces ß-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.

Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis.

Chromosome painting is a powerful technique for chromosome and genome studies. We developed a flexible chromosome painting technique based on multiplex PCR of a synthetic oligonucleotide (oligo) library in cucumber (Cucumis sativus L., 2n = 14). Each oligo in the library was associated with a universal as well as nested specific primers for amplification, which allow the generation of different probes from the same oligo library. We were also able to generate double-stranded labelled oligos, which produced much stronger signals than single-stranded labelled oligos, by amplification using fluorophore-conjugated primer pairs. Oligos covering cucumber chromosome 1 (Chr1) and chromosome 4 (Chr4) consisting of eight segments were synthesized in one library. Different oligo probes generated from the library painted the corresponding chromosomes/segments unambiguously, especially on pachytene chromosomes. This technique was then applied to study the homoeologous relationships among cucumber, C. hystrix and C. melo chromosomes based on cross-species chromosome painting using Chr4 probes. We demonstrated that the probe was feasible to detect interspecies chromosome homoeologous relationships and chromosomal rearrangement events. Based on its advantages and great convenience, we anticipate that this flexible oligo-painting technique has great potential for the studies of the structure, organization, and evolution of chromosomes in any species with a sequenced genome.

Analysis of Genetic Alterations Related to DNA Methylation in Testicular Germ Cell Tumors Based on Data Mining.

Embryonal carcinoma (EC) and seminoma (SE) are both derived from germ cell neoplasia in situ but show big differences in growth patterns and clinical prognosis. Epigenetic regulation may play an important role in the development of EC and SE. This study investigated the DNA methylation-based genetic alterations between EC and SE by analyzing the datasets of mRNA expression and DNA methylation profiling. The datasets were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified between EC and SE by limma package in R environment. Gene function enrichment analysis of the DEGs was performed on the DAVID tool, the results of which suggested differences in capability of pluripotency and genomic stability between EC and SE. The minfi package and wANNOVAR tool were used to identify differentially methylated genes. A total of 37 genes were discovered with both mRNA expression and the accordant DNA methylation changes. The findings were verified by the sequencing data from The Cancer Genome Atlas database, and Kaplan-Meier survival analysis was performed. Finally, 5 genes (PRDM1, LMO2, FAM53B, HCN4, and FAM124B) were found that showed both low expression and high methylation in EC, and were significantly associated with relapse-free survival. The findings of methylation-based genetic features between EC and SE might be helpful in studying the role of DNA methylation in cancer development.

Complete chloroplast genome sequencing and comparative analysis reveals changes to the chloroplast genome after allopolyploidization in Cucumis.

Allopolyploids undergo "genomic shock" leading to significant genetic and epigenetic modifications. Previous studies have mainly focused on nuclear changes, while little is known about the inheritance and changes of organelle genome in allopolyploidization. The synthetic allotetraploid Cucumis ×hytivus, which is generated via hybridization between C. hystrix and C. sativus, is a useful model system for studying cytonuclear variation. Here, we report the chloroplast genome of allotetraploid C. ×hytivus and its diploid parents via sequencing and comparative analysis. The size of the obtained chloroplast genomes ranged from 154 673 to 155 760 bp, while their gene contents, gene orders, and GC contents were similar to each other. Comparative genome analysis supports chloroplast maternal inheritance. However, we identified 51 indels and 292 SNP genetic variants in the chloroplast genome of the allopolyploid C. ×hytivus relative to its female parent C. hystrix. Nine intergenic regions with rich variation were identified through comparative analysis of the chloroplast genomes within the subgenus Cucumis. The phylogenetic network based on the chloroplast genome sequences clarified the evolution and taxonomic position of the synthetic allotetraploid C. ×hytivus. The results of this study provide us with an insight into the changes of organelle genome after allopolyploidization, and a new understanding of the cytonuclear evolution.

Unique miRNAs and their targets in tomato leaf responding to combined drought and heat stress.

BACKGROUND: Both drought and heat stress are serious global problems, leading to agricultural production loss. MicroRNAs (miRNAs) play important roles in plant species responding to individual drought and heat stress. However, the miRNAs and mRNAs in association with combined drought and heat in crops like tomato remains unclear. RESULTS: We studied the crosstalk of miRNAs and their target genes in tomato plants grown under simultaneous drought and heat stress that frequently happen in field conditions. In total, 335 known miRNAs representing 55 miRNA families and 430 potential novel miRNAs were identified in Solanum lycopersicum L. using small RNA deep sequencing. Through expression analysis, miRNAs in association with drought, heat and the combination of these were investigated. In total, 61, 74 and 37 miRNAs were differentially regulated for combination (of both stresses) vs control, combination vs drought and combination vs heat, respectively. Target genes with different expression levels were found using degradome sequencing, which were mainly involved in transcription factor activity, sequence-specific DNA binding, transcription, regulation of transcription, nucleus, DNA binding etc. The quantitative real-time polymerase chain reaction (qRT-PCR) results confirmed the accuracy of sequencing. CONCLUSIONS: Our study serves as valuable knowledge on how crop adapted to combined drought and heat stress by regulating miRNAs and mRNAs, which provide information for crop improvement to deal with future climate changes.

Interactive effects of elevated CO2 concentration and combined heat and drought stress on tomato photosynthesis.

BACKGROUND: Extreme weather events are predicted to increase, such as combined heat and drought. The CO2 concentration ([CO2]) is predicted to approximately double by 2100. We aim to explore how tomato physiology, especially photosynthesis, is affected by combined heat and drought under elevated [CO2] (e [CO2]). RESULTS: Two genotypes, 'OuBei' ('OB', Solanum lycopersicum) and 'LA2093' (S. pimpinellifolium) were grown at a [CO2] (atmospheric [CO2], 400 ppm) and e [CO2] (800 ppm), respectively. The 27-days-old seedlings were treated at 1) a [CO2], 2) a [CO2] + combined stress, 3) e [CO2] and 4) e [CO2] + combined stress, followed by recovery. The PN (net photosynthetic rate) increased at e [CO2] as compared with a [CO2] and combined stress inhibited the PN. Combined stress decreased the Fv/Fm (maximum quantum efficiency of photosystem II) of 'OB' at e [CO2] and that of 'LA2093' in regardless of [CO2]. Genotypic difference was observed in the e [CO2] effect on the gas exchange, carbohydrate accumulation, pigment content and dry matter accumulation. CONCLUSIONS: Short-term combined stress caused reversible damage on tomato while the e [CO2] alleviated the damage on photosynthesis. However, the e [CO2] cannot be always assumed have positive effects on plant growth during stress due to increased water consumption. This study provided insights into the physiological effects of e [CO2] on tomato growth under combined stress and contributed to tomato breeding and management under climate change.

The Alleviation of Photosynthetic Damage in Tomato under Drought and Cold Stress by High CO2 and Melatonin.

The atmospheric CO2 concentration (a[CO2]) is increasing at an unprecedented pace. Exogenous melatonin plays positive roles in the response of plants to abiotic stresses, including drought and cold. The effect of elevated CO2 concentration (e[CO2]) accompanied by exogenous melatonin on plants under drought and cold stresses remains unknown. Here, tomato plants were grown under a[CO2] and e[CO2], with half of the plants pre-treated with melatonin. The plants were subsequently treated with drought stress followed by cold stress. The results showed that a decreased net photosynthetic rate (PN) was aggravated by a prolonged water deficit. The PN was partially restored after recovery from drought but stayed low under a successive cold stress. Starch content was downregulated by drought but upregulated by cold. The e[CO2] enhanced PN of the plants under non-stressed conditions, and moderate drought and recovery but not severe drought. Stomatal conductance (gs) and the transpiration rate (E) was less inhibited by drought under e[CO2] than under a[CO2]. Tomato grown under e[CO2] had better leaf cooling than under a[CO2] when subjected to drought. Moreover, melatonin enhanced PN during recovery from drought and cold stress, and enhanced biomass accumulation in tomato under e[CO2]. The chlorophyll a content in plants treated with melatonin was higher than in non-treated plants under e[CO2] during cold stress. Our findings will improve the knowledge on plant responses to abiotic stresses in a future [CO2]-rich environment accompanied by exogenous melatonin.

Allopolyploidization in Cucumis contributes to delayed leaf maturation with repression of redundant homoeologous genes.

The important role of polyploidy in plant evolution is widely recognized. However, many questions remain to be explored to address how polyploidy affects the phenotype of the plant. To shed light on the phenotypic and molecular impacts of allopolyploidy, we investigated the leaf development of a synthesized allotetraploid (Cucumis × hytivus), with an emphasis on chlorophyll development. Delayed leaf maturation was identified in C. × hytivus, based on delayed leaf expansion, initial chlorophyll deficiency in the leaves and disordered sink-source transition. Anatomical observations also revealed disturbed chloroplast development in C. ×hytivus. The determination of chlorophyll biosynthesis intermediates suggested that the chlorophyll biosynthesis pathway of C. × hytivus is blocked at the site at which uroporphyrinogen III is catalysed to coproporphyrinogen III. Three chlorophyll biosynthesis-related genes, HEMA1, HEME2 and POR, were significantly repressed in C. × hytivus. Sequence alignment showed both synonymous and non-synonymous substitutions in the HEMA1, HEME2 and POR genes of the parents. Cloning of the chlorophyll biosynthetic genes suggested the retention of homoeologs. In addition, a chimeric clone of the HEMA1 gene that consisted of homologous genes from the parents was identified in C. × hytivus. Overall, our results showed that allopolyploidization in Cucumis has resulted in disturbed chloroplast development and reduced chlorophyll biosynthesis caused by the repressed expression of duplicated homologous genes, which further led to delayed leaf maturation in the allotetraploid, C. × hytivus. The preferential retention/loss of certain types of genes and non-reciprocal homoeologous recombination were also supported in the present study, which provides new insights into the impact of allopolyploidy.

Key candidate genes associated with BRAFV600E in papillary thyroid carcinoma on microarray analysis.

The mechanisms of B-type Raf kinase (BRAF) V600E mutation in papillary thyroid cancer (PTC) remain to be elucidated. With the aim to investigate the key candidate genes distinctive to BRAFV600E -PTC, we analyzed the transcriptomics data from three microarray datasets (GSE27155, GSE54958, and GSE58545) and identified 491 differentially expressed genes (DEGs) between BRAFV600E -PTC and BRAFwild type -PTC. Functional enrichment analysis of DEGs revealed that negative regulation of wound healing may be involved in the BRAFV600E -related pathogenesis in PTC. Weighted gene coexpression network analysis revealed BRAFV600E -related coexpressed genes in PTC, from which hub genes were selected. The intersection of DEGs and hub genes revealed 31 candidates, wherein GRB7, SNAP25, SLC35F2, FAM155B, HGD, and ITPR1 were rendered the key candidate genes via receiver operating characteristic curve analysis. On further characterization, the six key genes displayed significantly different expression patterns at different cytomorphology, however, with no significant difference in overall survival. These results provide novel insights into the key genes distinctive to of BRAFV600E in PTC and might be suggestive as therapeutic targets for further application.

Physiological analysis and transcriptome sequencing reveal the effects of combined cold and drought on tomato leaf.

BACKGROUND: Co-occurrence of cold and drought stress can alter the response of plants at morphological, physiological and molecular levels, which finally affect crop production, more than individual stress. Understanding the responses of crop to combined stress is necessary to improve tolerance and maintain crop production especially in the field where combined stress frequently occurs. We aimed to clarify the underlying leaf physiological and molecular mechanisms of tomato by imposing combining cold and drought on one popular tomato cultivar 'Jinlingmeiyu' as an example. RESULTS: The physiological and genetic responses were identified in tomatoes after 42 h exposure to control, cold, drought and combined treatments. As compared with control, water loss rate at the three stresses including cold, drought and combined stress significantly decreased until 40 min after taking samples from the plants. The content of H2O2, zeatin riboside (ZR) and melatonin in all stress treatments were significantly higher than the control. Drought stress alone and combined stress induced the accumulation of abscisic acid (ABA) and auxin (IAA) as compared with control. The individual cold and combined stress significantly decreased the maximum quantum efficiency of PSII (Fv/Fm), quantum yield of PSII (Fq'/Fm') and electron transport rate (ETR). In total, 7141, 1850 and 7841 genes were involved in the stress response to cold, drought and their combination. Functional analysis of the stress-inducible genes provided more insights concerning the complex regulatory mechanisms that were involved in combined stress. The expression level of 12 genes were validated by quantitative real-time PCR (qRT-PCR). CONCLUSIONS: We found that the expression of stress-specific genes changed with physiological variation, indicating the close crosstalk between physiological and genetic response especially under combined stress. This study provides new knowledge on the complex regulatory mechanism genes in tomato ('Jinlingmeiyu') leaf to abiotic stresses.

Oligo-painting and GISH reveal meiotic chromosome biases and increased meiotic stability in synthetic allotetraploid Cucumis ×hytivus with dysploid parental karyotypes.

BACKGROUND: Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid parental karyotypes have not been studied in detail. The allotetraploid Cucumis ×hytivus (HHCC, 2n = 38) was obtained from interspecific hybridization between C. sativus (CC, 2n = 14) and C. hystrix (HH, 2n = 24) followed by chromosome doubling. The results of this study thus offer an excellent opportunity to explore the meiotic properties of allopolyploids with dysploid parental karyotypes. RESULTS: In this report, we describe the meiotic properties of five chromosomes (C5, C7, H1, H9 and H10) and two genomes in interspecific hybrids and C. ×hytivus (the 4th and 14th inbred family) through oligo-painting and genomic in situ hybridization (GISH). We show that 1) only two translocations carrying C5-oligo signals were detected on the chromosomes C2 and C4 of one 14th individual by the karyotyping of eight 4th and 36 14th plants based on C5- and C7-oligo painting, and possible cytological evidence was observed in meiosis of the 4th generation; 2) individual chromosome have biases for homoeologous pairing and univalent formation in F1 hybrids and allotetraploids; 3) extensive H-chromosome autosyndetic pairings (e.g., H-H, 25.5% PMCs) were observed in interspecific F1 hybrid, whereas no C-chromosome autosyndetic pairings were observed (e.g. C-C); 4) the meiotic properties of two subgenomes have significant biases in allotetraploids: H-subgenome exhibits higher univalent and chromosome lagging frequencies than C-subgenome; and 5) increased meiotic stability in the S14 generation compared with the S4 generation, including synchronous meiosis behavior, reduced incidents of univalent and chromosome lagging. CONCLUSIONS: These results suggest that the meiotic behavior of two subgenomes has dramatic biases in response to interspecific hybridization and allopolyploidization, and the meiotic behavior harmony of subgenomes is a key subject of meiosis evolution in C. ×hytivus. This study helps to elucidate the meiotic properties and evolution of nascent allopolyploids with the dysploid parental karyotypes.

Inhibition of Euchromatic Histone Lysine Methyltransferase 2 (EHMT2) Suppresses the Proliferation and Invasion of Cervical Cancer Cells.

EHMT2 (euchromatic histone lysine methyltransferase 2), a histone methyltransferase, has been shown to be involved in multiple human cancers. In this study, we determined mRNA and protein expression of EHMT2 in cervical cancer cells and normal cervical epithelial cells. EHMT2 was inhibited with short hairpin RNA (shEHMT2) in cervical cancer cells. Cell viability, colony proliferation, apoptosis, adhesion, and invasion assays and Western blot were performed to assess the function of EHMT2. As a result, EHMT2 was upregulated in human cervical cancer cells compared to normal cervical epithelial cells. Suppression of EHMT2 expression impairs cell proliferation and induces apoptosis. Furthermore, EHMT2 silencing inhibited cell adhesion and invasion. Finally, knockdown of EHMT2 resulted in a reduction of the expression of the tumorigenic proteins Bcl-2, Mcl-1, and Survivin and in an increase in the expression of the anti-malignant protein E-cadherin. In conclusion, our data suggest that EHMT2 plays a key role in cell proliferation and metastatic capacity in cervical cancer cells and could serve as a potential therapeutic target.

Candidate genes underlying the quantitative trait loci for root-knot nematode resistance in a Cucumis hystrix introgression line of cucumber based on population sequencing.

The southern root-knot nematode (RKN), Meloidogyne incognita (Kofoid & White) Chitwood, is one of most destructive species of plant parasitic nematodes, causing significant economic losses to numerous crops including cucumber (Cucumis sativus L. 2n = 14). No commercial cultivar is currently available with resistance to RKN, severely hindering the genetic improvement of RKN resistance in cucumber. An introgression line, IL10-1, derived from the interspecific hybridization between the wild species Cucumis hystrix Chakr. (2n = 24, HH) and cucumber, was identified with resistance to RKN. In this study, an ultrahigh-density genetic linkage bin-map, composed of high-quality single-nucleotide polymorphisms (SNPs), was constructed based on low-coverage sequences of the F2:6 recombinant inbred lines derived from the cross between inbred line IL10-1 and cultivar 'Beijingjietou' CC3 (hereinafter referred to as CC3). Three QTLs were identified accounting for 13.36% (qRKN1-1), 9.07% and 9.58% (qRKN5-1 and qRKN5-2) of the resistance variation, respectively. Finally, four genes with nonsynonymous SNPs from chromosome 5 were speculated to be the candidate RKN-resistant related genes, with annotation involved in disease resistance. Though several gaps still exist on the bin-map, our results could potentially be used in breeding programs and establish an understanding of the associated mechanisms underlying RKN resistance in cucumber.